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<!doctype html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>ChEMBL beaker</title>
<meta name="description" content="Web based presentation providing an update on Beaker server.">
<meta name="author" content="Michał Nowotka">
<meta name="apple-mobile-web-app-capable" content="yes"/>
<meta name="apple-mobile-web-app-status-bar-style" content="black-translucent"/>
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<link rel="stylesheet" href="css/reveal.css">
<link href="http://www.ebi.ac.uk/favicon.ico" rel="icon"/>
<link rel="stylesheet" href="css/theme/zen.css" id="theme">
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<script>
document.write('<link rel="stylesheet" href="css/print/' + ( window.location.search.match(/print-pdf/gi) ? 'pdf' : 'paper' ) + '.css" type="text/css" media="print">');
</script>
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<script src="lib/js/html5shiv.js"></script>
<![endif]-->
</head>
<body>
<div class="reveal">
<div class="slides">
<section>
<h3>Using RDKit <br />without RDKit</h3>
<img src="img/beaker.png" style="position:fixed;left:1%;top:2%;">
<p style="font-size:22pt;">Beaker update</p>
<p>
<small>Michał Nowotka<br/>ChEMBL Group<br/>EMBL-EBI</small>
</p>
</section>
<section>
<h3>What is Beaker?</h3>
<p class="fragment">
Remote RDKit (and OSRA) accessible over HTTP from the Internet or locally.
</p>
</section>
<section>
<h3>Can you be more specific?</h3>
<p>
<ul>
<li class="fragment">A lightweight web framework</li>
<li class="fragment">Written in Python</li>
<li class="fragment">Based on Bottle</li>
<li class="fragment">Exposing REST API</li>
<li class="fragment">Providing cheminformatics services</li>
<li class="fragment">Easy to extend and modify</li>
</ul>
</p>
</section>
<section>
<h3>What has changed?</h3>
<p>
<ul>
<li class="fragment">Beaker was first presented a year ago</li>
<li class="fragment">It's not a pet project anymore</li>
<li class="fragment">Production ready</li>
<li class="fragment">In fact, used in production already!</li>
</ul>
</p>
</section>
<section>
<h3>What's new then?</h3>
<p>
<ul>
<li class="fragment">Live online documentation</li>
<li class="fragment">Better configuration</li>
<li class="fragment">Caching system</li>
<li class="fragment">Throttling system</li>
<li class="fragment">Authentication</li>
<li class="fragment">Better security</li>
<li class="fragment">New methods</li>
</ul>
</p>
</section>
<section>
<h3>What's new then?</h3>
<p>
<ul>
<li class="fragment">mod_wsgi ready (Apache, NGINX)</li>
<li class="fragment">Python client library</li>
<li class="fragment">Development server improved</li>
<li class="fragment">Lots of bugfixes</li>
<li class="fragment">Easier to extend/write own methods</li>
</ul>
</p>
</section>
<section>
<h3>How to install it?</h3>
<pre class="fragment"><code class="bash">
sudo pip install chembl_beaker
</code></pre>
</section>
<section>
<h3>Can I use it without installing?</h3>
<h6 class="fragment">Yes!</h6>
<h3 class="fragment">Yes!!</h3>
<h1 class="fragment">Yes!!!</h1>
</section>
<section>
<h3>Beaker availability:</h3>
<p>
<ul>
<li class="fragment">PyPi (`pip install chembl_beaker`)</li>
<li class="fragment">myChEMBL</li>
<li class="fragment"><a href="https://www.ebi.ac.uk/chembl/api/utils/docs" target="_blank" >online</a></li>
</ul>
</p>
</section>
<section>
<h3>Using Beaker from myChEMBL:</h3>
<pre class="fragment"><code class="bash">
vagrant init chembl/myChEMBL
vagrant up
</code></pre>
</section>
<section>
<h3>Using public instance of Beaker:</h3>
<p>
<ul>
<li class="fragment">IP-based rate limiting: 1 request per sec</li>
<li class="fragment">You can ask for an API key</li>
<li class="fragment"><a href="https://www.ebi.ac.uk/chembl/api/utils/docs" target="_blank" >https://www.ebi.ac.uk/chembl/api/utils/docs</a></li>
<li class="fragment">as an addition to: <a href="https://www.ebi.ac.uk/chemblws/docs" target="_blank" >https://www.ebi.ac.uk/chemblws/docs</a></li>
</ul>
</p>
</section>
<section>
<h3>For Python, we provide a very convenient client library:</h3>
<pre class="fragment"><code class="bash">
pip install chembl-webresource-client
</code></pre>
</section>
<section>
<h3>Beaker client library:</h3>
<p>
<ul>
<li class="fragment">Caches results</li>
<li class="fragment">Generates methods from SPORE specs</li>
<li class="fragment">By default uses public instance of Beaker...</li>
<li class="fragment">... but can be configured</li>
<li class="fragment">Described in 07_* my_ChEMBL python notebook</li>
</ul>
</p>
</section>
<section>
<h3>Potential use cases:</h3>
<p>
<ul>
<li class="fragment">Web widgets</li>
<li class="fragment">Mobile applications</li>
<li class="fragment">Desktop applications</li>
<li class="fragment">Ipython notebooks</li>
<li class="fragment">Fast prototyping</li>
<li class="fragment">Marvin 4 JS backend</li>
</ul>
</p>
</section>
<section>
<h3>Caching backends:</h3>
<p>
<ul>
<li class="fragment">MongoDB (for production)</li>
<li class="fragment">Memcached (for production)</li>
<li class="fragment">SQLite (for testing)</li>
<li class="fragment">Local memory (for testing)</li>
<li class="fragment">Your own?</li>
</ul>
</p>
</section>
<section>
<h3>Throttling backends:</h3>
<p>
<ul>
<li class="fragment">Cache</li>
<li class="fragment">Your own?</li>
</ul>
</p>
</section>
<section>
<h3>Authentication:</h3>
<p>
<ul>
<li class="fragment">IP based</li>
<li class="fragment">API Key</li>
<li class="fragment">Your own?</li>
</ul>
</p>
</section>
<section>
<h3>Security:</h3>
<p>
<ul>
<li class="fragment">Cross-origin requests controlled</li>
<li class="fragment">Rate limiting (DDOS)</li>
<li class="fragment">No persistence, no SQL injection</li>
<li class="fragment">URL-safe base64 encoding for url parameters</li>
<li class="fragment">IP white/black listing</li>
<li class="fragment">Maximum file upload size (configurable)</li>
</ul>
</p>
</section>
<section>
<h2>Future</h2>
<ul>
<li class="fragment">Sessions</li>
<li class="fragment">Parallel processing</li>
<li class="fragment">More support for creating pipelines...</li>
<li class="fragment">...KNIME like web interface?</li>
<li class="fragment">Windows binary</li>
<li class="fragment">ReadTheDocs documentation and separate website</li>
<li class="fragment">Improved live docs</li>
</ul>
</section>
<section>
<h2>Code!</h2>
<p>Beaker code is available as github repository:
<br/>
<a href="https://github.com/mnowotka/chembl_beaker">https://github.com/mnowotka/chembl_beaker</a>
<br/>
</p>
</section>
<section>
<h2>Thank you!</h2>
<p>Questions?</p>
</section>
</div>
</div>
<footer>
<div style="">
<a href="mailto:[email protected]">[email protected]</a>
<img src="img/ebi_logo.png"/>Darmstadt, 23 October 2014
</div>
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